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Cell Systems February 16, 2022; PMID: 34637888

The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner

Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E


iScience January 18, 2022; PMID: 35141507

Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues.

Kubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin DJ, Duquette JD, Kovalchik KA, Wessling L, Kohlbacher O, Rammensee HG, Neidert MC, Sirois I, Caron E


STAR Protocols October 21, 2021; PMID: 34746858

RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery

Saab F, Hamelin DJ, Ma Q, Kovalchik KA, Sirois I, Faridi P, Li C, Purcell AW, Kubiniok P, Caron E


Molecular & Cellular Proteomics November 17, 2021; PMID: 34798331

MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets

Kovalchik K, Ma Q, Wessling L, Saab F, Duquette JD, Kubiniok P, Hamelin DJ, Faridi P, Li C, Purcell AW, Jang A, Paramithiotis E, Tognetti M, Reiter L, Bruderer R, Lanoix J, Bonneil E, Courcelles M, Thibault P, Caron E, Sirois I

J. Vis. Exp. October 15, 2021; PMID: 34723952

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Sirois I, Isabelle M, Duquette JD, Saab F, Caron E


Molecular & Cellular Proteomics January 01, 2020

The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases


Vizcaíno JA, Kuniok P, Kovalchik K, Ma Q, Despault J, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I and Caron E 


Sci Data 2018, 5:180157

A tissue-based draft map of the murine
MHC class I immunopeptidome


Schuster H, Shao W, Weiss T, Pedrioli P, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Rammensee HG, Aebersold R*, Caron E*

*Co-corresponding author

Nucleic Acids Research - 2018, 46 (D1):D1237-D1247

The SysteMHC Atlas project


Shao W, Pedrioli P, Wolski W, Scurtescu C, Schmid E, Vizcaino JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R*, and Caron E*

*Co-corresponding author

Immunity - 2017, 47:203-208.

A Case for a Human Immuno-Peptidome Project Consortium

Caron E§*, Aebersold R, Banaei-Esfahani A, Chong C, Bassani-Sternberg M*

§Lead contact,*Co-corresponding author

Cell Reports - 28 March 2017, 18(13):3219-3226

Precise temporal profiling of protein signaling complexes in primary cells using SWATH mass spectrometry


Caron E*, Roncagalli R*, Takeshi H, Wolski WE, Meena C, Menoita MG, Durand S, Garcia-Blesa A, Fierro-Monti I, Sajic T, Heusel M, Weiss T, Malissen M, Schlapbach R, Collins B, Ghosh S, Kitano H, Aebersold R, Malissen B, Gstaiger M.  

*Co-first author


Mol Cell Proteomics - December 2015, 14(12):3105-17

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry


Caron E, Kowalewski DJ, Chiek Koh C, Sturm T, Schuster H, Aebersold R 


eLife - 2015, 4:e07661

An open-source computational and data resource to analyze quantitative digital maps of immunopeptidomes


Caron E*, Espona L, Kowalewski D, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Lindestam CSA, Koh CC, Gillet L, Rabsteyn A, Sturm T, Navarro P, Kim S, Lam H, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R* 

*Co-corresponding author

Nature - 2014, 515:577-581

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens


Gubin MM, Zhang X, Schuster H, Caron E, Noguchi T, Ward JP, Ivanova Y, Hundal J, Arthur CD, Krebber WJ, Mulder GE, Vesely MD, Lam SSK, Korman AJ, Allison JP, Freeman GJ, Sharpe AH, Pearce EL, Aebersold R, Rammensee HG, Melief CJM, Mardis ER, Gillanders WE, Artyomov MN, Schreiber RD

Molecular System Biology - 2011, 7:753

The MHC class I immunopeptidome conveys to the cell surface an integrative view of cellular regulation

Caron E*, Vincent K*, Fortier MH*, Laverdure JP, Bramoullé A, Hardy MP, Voisin G, Roux PP, Lemieux S, Thibault P, Perreault C.

*Co-first author

Molecular System Biology -  2010, 6:453

A comprehensive map of the mTOR signaling network


Caron E, Ghosh S, Matsuoka Y, Ashton-Beaucage D, Therrien M, Lemieux S, Perreault C, Roux PP, Kitano H


Journal of Experimental Medicine - 2008, 205:595-610

The MHC class I peptide repertoire is molded by the transcriptome

Fortier MH*, Caron E*, Hardy MP, Voisin G, Lemieux S, Perreault C, Thibault P

*Co-first author


ASBMB Today November 11, 2021

Pondering the power of connections in the post–COVID-19 era

Caron E

Book Chapter

Methods Mol Biol. 2022; PMID: 34905171

Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS


Kovalchik K, Hamelin D, Caron E

Book Chapter

Methods Mol Biol. 2020; PMID: 32124319

The SysteMHC Atlas: a Computational Pipeline, a Website, and a Data Repository for Immunopeptidomic Analyses


Shao W, Caron E, Pedrioli P, Aebersold R

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